Earlier studies yielded inconsistent results on the association between variation in the serotonin transporter (5-HTT) gene and depression, with evidence for a differential effect of the 5-HTTLPR on melancholic versus atypical depression. To further delineate the impact of 5-HTT gene variation on psychopathology in depression, in this analysis the influence of the 5-HTTLPR and the functionally closely related 5-HTT rs25531 was investigated in 340 Caucasian patients with a major depressive episode (DSM-IV) with particular attention to the subtype of depression (melancholic depression versus atypical depression) applying logistic regression models adjusted for age and gender. The homozygous, more active 5-HTTLPR LL genotype was significantly associated with melancholic depression (odds ratio, OR, 1.7; 95% confidence interval, CI, 1.1-2.6; P=0.04), with the effect originating in the female subgroup of patients (OR 1.9; 95%CI 1.0-3.4; P=0.05). Also, the more active 5-HTTLPR/5-HTT rs25531 haplotype L(A)L(A) conveyed a significant risk for melancholic depression (OR 2.0; 95%CI 1.3-3.1; P=0.001), again only in the female subsample of patients (OR 2.1; 95%CI 1.1-4.1; P=0.02). The present results provide further support for an association of genetic variation increasing serotonin transporter activity with the melancholic subtype of depression as well as evidence for a potential female-specific mechanism underlying this effect.